Suppressive soils have been identified as soils that can inhibit the growth of naturally occurring soil-borne diseases. These soils contain microbial communities that are capable of suppressing or controlling disease-causing organisms, including fungi (e.g. Fusarium virguliforme (cause of sudden death syndrome, SDS), Macrophomina phaseolina (cause of charcoal rot), Phytophthora root rot (Phytophthora sojae) and nematodes (e.g., soybean cyst nematode, Heterodera glycines). How the native soil microbial communities reduce disease is not known. Knowledge of factors that contribute to and support these beneficial microbial communities is also unknown.

One example of this natural improvement in soil microbial community reducing disease was demonstrated in our previous research (Sassenrath et al., 2017, 2019; sponsored by the Kansas Soybean Commission) that demonstrated that a high-glucosinolate mustard (Brassica juncea) reduced fungal populations that caused charcoal rot in soil and in soybean plants. The research proposed here builds on those results by exploring the interaction between soil health and disease pressure. Management practices will be tested in field studies to determine the impact on soil health, fungal pathogen presence, and soybean growth and yield.

Impact of soil health on soybean disease.
Crop plants that are disease hosts increase the number of disease-causing organisms in the soil. We have previously shown the increase in colony forming units (CFU) of M. phaseolina in the soil after soybean production (Sassenrath et al., 2019). Other factors reduce soil-borne disease, include high-glucosinolate mustard as a cover crop (Sassenrath et al., 2017, 2019) and increasing the soil temperature (e.g., "solarization"). Use of animal manures greatly increases the diversity of the soil microbial community, and beneficial microorganisms in particular. In addition to improving the soil nutrient balance, manure may contribute to reduced disease pressure (Graham et al., 2014) and soybean cyst nematode populations (Bao et al., 2013). Background information on soil temperature and moisture will be collected continuously throughout the growing season using Hobo Temperature and Moisture sensors installed in each treatment. These sensors are purchased with funds from complimentary grant programs.

Measuring the impact of soybean health on soybean diseases.
Management practices to alter the soil community structure will be implemented in replicated research plots at the Southeast Research and Extension Center fields in Parsons, KS. Treatments will include two treatments that are likely to increase disease (soybeans and corn stubble, both hosts of disease organisms), three treatments that are likely to decrease disease (brassica cover crop, animal manure, and solarization), and a fallow control. We will also be testing different soybean cultivars from MG 3.5 – 4.9 with different susceptibilities to disease. The soybean variety test plots at Ottawa will also be sampled to measure differences in plant and soil disease for MG 3.5 and MG 4.9. Additional test sites include sixteen fields at production farmers in eastern Kansas.

Testing will include several cultivars of soybeans with noted sensitivity to charcoal rot and sudden death (disease susceptibility: 9 = excellent; 1 = poor.):
Cultivar Maturity Group SCN Resistance Source Phytophthora resistance gene Sudden Death Syndrome Susceptibility Charcoal Rot Susceptibility
P35T15E 3.5 P188788 1k 5 4
P38454E 3.8 P188788 1a 7 8
P42T31E 4.2 P188788 - 5 4
P45T88E 4.5 P188788 ^1k 6 8
P49T74E 4.9 P188788 ^1c, ^1k 5 4
Phytophthora resistance gene: 1a: Provides resistance to races 1, 2, 10, 11, 13-18, 24, 26, 27, 31, 32 & 36. 1c: Provides resistance to races 1-3, 6-11, 13, 15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36. 1k: Provides resistance to races 1-11, 13-15, 17, 18, 21-24, 26, 36, 37. (-) no specific gene for resistance

Soils will be sampled at three times during the season to determine: soil nutrients, soil community structure, and pathogen populations. Soils will be sampled prior to implementation of treatments (early March), mid-season (late June-July) and after harvesting soybeans (Sept. – Oct.). Final soybean yield will be collected.

The Soil Management Assessment Framework has identified five factors that are indicative of soil microbial activity. SMAF has been adopted by the NRCS as an indicator of soil health. These factors include: organic carbon, nitrogen, active carbon, wet aggregate stability, and soil respiration. These factors give an indication of the activity of the soil microbiome, though they do not measure the microbes directly. Total microbial biomass and the ratio of fungi to bacteria have also been shown to be related to disease suppression in soils.

Soil nutrients are important for growth of both microbes and plants. These will be measured at the K-State Soil Testing Lab, and include: pH, total organic matter, N, P, K, total organic carbon, total N, NO3-N, NH4-N, along with key micronutrients S, Ca, Mg, and Na. Wet aggregate stability will be measured using the soil volumetric aggregate stability test (VAST) from Solvita. Soil respiration will be measured with the CO2 Burst Test by Solvita. In addition, we will quantitate the disease presence of Macrophomina in soil and plants at three time points during the growing season (prior to planting, mid-season, and at harvest) by measuring CFUs.

This past year, we tested total soil microbial biomass and fungal:bacterial ratio with the MicroBIOMETER system. Unfortunately, results were not clear, and the test was disappointing. An examination of other potential disease organisms would be possible through PCR tests with disease-specific primers. This test would give a qualitative measure of disease presence and, in addition to Macrophomina, and allow detection of Fusarium, Phytophthora, Phomopsis, and Pythium. This analysis is expensive and beyond the scope of this proposal. We have submitted a funding request to SARE to pursue this research. We will continue to explore methods and funding sources to measure and quantitate total soil microbial biomass and fungal:bacterial ratios, and detection of disease organisms as an indication of “soil health”.

M. phaseolina populations will be determined by counting the number of colony-forming units (CFUs). Charcoal rot disease severity will be measured by randomly selecting ten plants per plot at the R7-R8 growth stage for root and stem severity ratings. The plants will be scored by splitting the stem and taproot of each plant and rating the degree of gray discoloration and microsclerotia in the vascular and cortical tissues on a scale of 1-5. M. phaseolina root populations will be estimated by grinding the split roots after the severity evaluation. The ground plant tissue and soil samples will be plated on microbiological media and incubated. CFUs of M. phaseolina will be counted and transformed to CFUs per gram of root tissue or gram of soil.

Identification of management practices, including cover crops, residue management, and animal manures, for use in biocontrol of soil-borne diseases and development of guidelines for economical management practices will assist producers in controlling fungal diseases in soybean. The impact of fungicide use on yield and net return will be determined, and guidelines developed. The interaction between soil health and fungal pressure will be assessed and alternative methods of improving soil health for optimal soybean production, yield components, and net return developed. The economic impact of management choices will assist producers in choosing economically viable production systems.
This research is a component of a project exploring the mechanisms defining how soil health impacts crop production and plant disease. The research team has developed a proposal to leverage KSC funding with national funding through SARE. That research will focus on development of the DNA technology to identify and quantify disease organizations. If funded, that research will contribute to this research by expanding our knowledge of specific disease organisms and quantities under different conditions. This research is exploring the interactions between soil health and crop performance, developing alternative methods to control crop diseases and establish naturally disease-suppressive soils through cultural practices.

Diseases are primary factors reducing the yield and quality of soybeans in Kansas and throughout the world. Soil-borne diseases are highly prevalent in eastern Kansas crop fields. Certain plants have been shown to produce chemicals that act as biofumigants that control or reduce harmful soil fungi. Animal manures have also been used to alter the soil microbiome to improve control of disease organisms. Our working hypothesis is that improving the overall soil health by supporting healthy soil microbial communities can reduce disease pressure, i.e. creating suppressive soils by altering management practices will reduce disease pressure. This research will explore the relationship between soil health and disease pressure. The research outlined here will test the ability of cover crops, animal manure, and solarization to control charcoal rot in soybean production through improved soil microbial communities.